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- PDB-7jje: Sarcin-ricin loop with guanosine dithiophosphate residue. -

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Basic information

Entry
Database: PDB / ID: 7jje
TitleSarcin-ricin loop with guanosine dithiophosphate residue.
ComponentsRNA (27-MER)
KeywordsRNA / Sarcin-ricin loop / RNA crystal structure / RNA tetraloops
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsPallan, P.S. / Egli, M. / Harp, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Biochemistry / Year: 2020
Title: Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost.
Authors: Pallan, P.S. / Lybrand, T.P. / Schlegel, M.K. / Harp, J.M. / Jahns, H. / Manoharan, M. / Egli, M.
History
DepositionJul 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)8,7781
Polymers8,7781
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.581, 29.581, 76.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: RNA chain RNA (27-MER)


Mass: 8778.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Crystallization set-ups were made by mixing 4 uL of 350 uM RNA solution [1 mM Na 2 EDTA (pH 8.0) and 10 mM Tris-HCl (pH 8.0)] with 2 uL of a crystallization buffer composed of 3.0 M ammonium ...Details: Crystallization set-ups were made by mixing 4 uL of 350 uM RNA solution [1 mM Na 2 EDTA (pH 8.0) and 10 mM Tris-HCl (pH 8.0)] with 2 uL of a crystallization buffer composed of 3.0 M ammonium sulfate, 10 mM magnesium chloride, 10 mM manganese chloride, and 50 mM potassium 3-(N-morpholino) propanesulfonic acid (MOPS), pH 7.0 at 18 C.
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 10, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.551
11-K, -H, -L20.449
ReflectionResolution: 1.25→30 Å / Num. obs: 18152 / % possible obs: 99.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.028 / Net I/σ(I): 40.06
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.76 / Num. unique obs: 1812 / Rpim(I) all: 0.239 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 3S7C

3s7c


Resolution: 1.25→27.6 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.684 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.008 / ESU R Free: 0.008 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1478 901 5 %RANDOM
Rwork0.1103 ---
obs0.1122 17225 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.96 Å2 / Biso mean: 15.641 Å2 / Biso min: 6.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å2-0 Å2-0 Å2
2---1.63 Å2-0 Å2
3---3.26 Å2
Refinement stepCycle: final / Resolution: 1.25→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 579 0 98 677
Biso mean---26.48 -
Num. residues----27
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.011701
X-RAY DIFFRACTIONr_bond_other_d00.02286
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.3311092
X-RAY DIFFRACTIONr_angle_other_deg1.673694
X-RAY DIFFRACTIONr_chiral_restr0.1090.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0280.02352
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02155
X-RAY DIFFRACTIONr_rigid_bond_restr6.4323987
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 81 -
Rwork0.14 1251 -
all-1332 -
obs--97.08 %

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